Not much is known about the plot, although it is very likely that actor Cillian Murphy will play Edward Dillinger, Jr. who may be the villain. Bruce Boxleitner has mentioned in an interview that he believes Disney will "get the ball rolling next year", and has confirmed rumors of Dillinger Jr. returning: "Let's just say...Cillian Murphy doesn't do cameos".

This rumor started with a leak about a TRON 3 teaser trailer that was supposedly going to be released with the DVD and Blu-Ray Discs in April 2011. Footage shot for the "teaser" has been certified by Disney, and some of it is featured inTRON: The Next Day - an exclusive 10-minute short depicting the history of the Flynn Lives movement and essentially bridging the gap between TRON,Legacy and a possible third instalment - which is only available on the Blu-Ray release of the film. The said release features another scene as one of the hidden "Easter Eggs" that are only on the US Blu-Ray. The scenes that are classified by fans as a link to TRON 3 are:

The first, which is featured in the closing minutes of The Next Day, features Roy Kleinberg (Dan Shor), the user of Ram from the original TRON, being confronted by Alan Bradley (Bruce Boxleitner). Kleinberg is revealed to be responsible for running the Flynn Lives campaign. Alan offers Ram a place at ENCOM, describing him as "ENCOM's moral compass".

The second scene was rumored to feature Quorra (Olivia Wilde) in the real world as she arrives at ENCOM Tower, where the press start to ask questions about Kevin Flynn's disappearance. She reveals that she did indeed meet Kevin the day prior. This scene was reported to be featured in The Next Day, only for her to be replaced with Sam in the final scene. In the final cut of the scene, Sam is seen arriving at ENCOM for his first board meeting, and when asked the question "Sam, do you have any statements for the press today?", he reveals his Flynn Lives t-shirt under his biker jacket, before the elevator doors close.

The third scene is a hidden "Easter Egg" only on the US Blu-Ray release, and shows Ed Dillinger Jr. chatting on the ENCOM ILC server with a second ambiguous character with the username "MCTRL_751", either his father or a new version of the MCP, who after the events of The Next Day warned Dillinger Jr. of Sam: "He may not be his father but he's still a Flynn. Don't underestimate him." and ending the communication with MCP's trademark "End of Line."

The co writers of TRON: Legacy were interviewed at the 2012 WonderCon about the third TRON film. They told them: "We are working on a sequel," said Adan Horowitz. "Eddie and I aren't writing the sequel -- because of the show [Once Upon a Time] we've moved to be co-producers on it. But there's a script being written right now." "Dave DiGilio is writing it," added Kitsis. "Joseph Kosinski is right now shooting Oblivion, but we've had a lot of meetings and conversations and we've seen the first draft of the Tron sequel." The two were asked about the possible return of Kevin Flynn. Adam Horowitz responded, "I would say the definition of life and death in the digital realm --" finished Kitsis, "Will be explored in the sequel!" Concerning the possible return of Quorra (played by Olivia Wilde in Legacy), Horowitz moved to the next roundtable.

In December of 2012, Jesse Wigutow was reported to be working on the latest version of the script, and Joseph Kosinski was interviewed about the movie, discussing such details as the movie's scale, in-universe lapse of time since Legacy, bringing new designs to the film, and possible involvement by Daft Punk.